Data processing workstations

Data Processing Workstations

Our users can use our powerful data processing workstations (remote access available). The users are obliged to acknowledge the laboratory and CZBI grant in the paper they used the data processed on our workstations - see the Acknowledgement section

Available software:

- FIJI/ImageJ – Image filtering, tomogram processing, data analysis, script based batch processing

- Microscopy Image Browser (MIB) – Image filtering, data analysis, script based batch processing, dataset alignment, image segmentation – manual/semi-automatic/deep-learning

- AMIRA – Image segmentation, model rendering, model animation

- Etomo – Tomogram reconstruction, serial sections analysis, image stitching,3D data filtering

- 3dmod – 3D data visualization, image segmentation, model rendering

- PEET – tomogram averaging (volume data)

- Matlab/Octave – image data analysis

- Chimera/ChimeraX – Electron density visualization and anaysis, combination of protein structures

- CryoSPARC – Single Particle Data Analysis from both cryo and negativ stain imaging

Contact persons for data processing: Týč Jiří, RNDr. Ph.D., František Kitzberger, Mgr., MSc., Bílý Tomáš Ph.D., Gardian Zdenko, Ing. Ph.D.
For the remote access, please contact the head of facility: Vancová Marie, RNDr. Ph.D.

Bookin slots on the workstations: How to book?, Booking calendar

Tha laboratory of electron microscopy has been connected to a powerful computational cluster, that serves as a data storage as well.

parameters of the cluster:

5TB RAM, 544/1088 CPU, 4x GPU Tesla V100S, dedicated space: 200 TB